Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_1CU-N1-BDNA-1_B23KGCJLT4_1/1029_1CU-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/8bf7c05e3a75e756624bc2e27a8194/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/8bf7c05e3a75e756624bc2e27a8194/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_1CU-N1-BDNA-1_B23KGCJLT4_1/1029_1CU-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_1CU-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_1CU-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1CU-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_1CU-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai

Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 81850375 total, 45478 skipped (flags/unmapped)
Fragments: 40997649 total (40776221 tlen-paired, 2079 hash-paired, 395 singletons, 10014 discordant, 208940 orphans, 9467 too large [>5000 bp], 14748890 duplicates)
Reads: 89739869 total, 49077 skipped (flags/unmapped)
Fragments: 44954261 total (44687912 tlen-paired, 2374 hash-paired, 371 singletons, 14357 discordant, 249247 orphans, 15944 too large [>5000 bp], 16518297 duplicates)
Reads: 76749109 total, 56439 skipped (flags/unmapped)
Fragments: 38441142 total (38212651 tlen-paired, 3893 hash-paired, 428 singletons, 14304 discordant, 209866 orphans, 10340 too large [>5000 bp], 14071981 duplicates)
Reads: 90377868 total, 78659 skipped (flags/unmapped)
Fragments: 45323600 total (44784521 tlen-paired, 1997 hash-paired, 388 singletons, 99501 discordant, 437193 orphans, 44795 too large [>5000 bp], 16678851 duplicates)